I'm guessing the rarity of such deals is often because there's too much of a difference in the two clubs' valuation of the makeweight.
The value of anything is what someone is prepared to pay. If, for example, we invited bids for Harry Wink of any price and then received none at all, not even a derisory £10,000, then Winks' value is effectively £0. So in this case Leicester would be justified in saying (from a financial point of view) that we were trying to get their highly-valued player at a cut price.
I imagine it's an issue in accounting terms, they have to record the asset that is Winks at "fair value", an auditor would want to know what his nominal fee was as part of the Maddison deal.